ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AATTTATGGAGTGCATGACGAATCCAAGGACAAAGCTTTTGAGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtgggaccagatattcaggcgaagaatggcctctctatgtttctcgatttgaatttaaagctgaaacttctttggtcacctgtcatacag

Basic information

species	Zea mays
transcript	GRMZM2G028346_T02
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G028346_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 10

AATTTATGGAGTGCATGACGAATCCAAGGACAAAGCTTTTGAGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtgggaccagatattcaggcgaagaatggcctctctatgtttctcgatttgaatttaaagctgaaacttctttggtcacctgtcatacag
 ||||||||||| ||||| ||| | ||||||||||||||||||||||| || |||||||| ||||||||||| || |||||||||||||||||    ||      | |||| |    |  |||   |||| |   | | |   | |||| ||          ||   ||||    ||| |||||||
CATTTATGGAGTACATGATGAAGCTAAGGACAAAGCTTTTGAGTTGGAATTAAGCTGGATATGTGATGAATCAAATCGCCAGCATCAGAAGgtgttctg----ttgttatttaaa-aataaataaactctgtccatatttt--tgtgaactttg--------ctcacttggcatactg-catacag

upper sequence: GRMZM2G028346_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA19G17920.1 (Glycine max), 5'ss of exon 9

AATTTATGGAGTGCATGACGAATCCAAGGACAAAGCTTTTGAGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtgggac-------cagatattcaggcgaaga-atggcctctctatgtttctcgatttgaatt-taaagctgaaacttctttggtcacctgtcatacag
 || |||||||| ||||||||  |||||||||||| ||| || || ||  |||||||| | ||||||||||| |||||||| ||| ||||||||  |  ||         | | || |    |    | |     | | |  ||| |   ||   |||  | ||  ||   | | | || | |  ||| ||    
TATATATGGAGTTCATGACGAGGCCAAGGACAAAGATTTCGAATTAGAAATGAGCTGGGTGTGTGATGAATCAAACCGCCAACATGAGAAGgtaaggctgggtgtactttcggttacttctacatgtagacaatttgtttcagttaccttatgacaatgatcaatgtgcttcatttgtgattagttgtaat----

upper sequence: GRMZM2G028346_T01 (Zea mays), 5'ss of exon 8
lower sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 9

AATTTATGGAGTGCATGACGAATCCAAGGACAAAGCTTTTGAGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtgggaccagatatt-caggcgaagaatggcctctctatgt-ttctcgatttgaatttaaagctgaaacttctt-tggtcacctgtcatacag
 || ||     | || || ||| |||||||||| |||||||| |||||| |||||||||| || || || || || ||  ||||||||||||||   |   |  ||   || |    |||| |||   |    |  | |||   |     || ||||   ||  | || | | |               
CATCTACAAGCTACACGATGAAGCCAAGGACAAGGCTTTTGAATTGGAGATGAGCTGGATATGCGAGGAGTCAAAACGAGAGCATCAGAAGgtaaaattttataagtgcttgcttatgaaggatgatttaaggagatattcataaaccatatataaattggactcgtcgtatag---------------

upper sequence: GRMZM2G028346_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv08s0040g00410.t01 (Vitis vinifera), 5'ss of exon 9

AATTTATGGAGTGCATGACGAATCCAAGGACAAAGCTTTTGAGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgta--ccgtgggaccagatattcaggcgaagaatggcctctctatgtttctcgatttgaatt-taaagctgaa-acttctttggtcacctgtcatacag-
 |||||||| || || || ||  |||||||||| || |||||||||||  |||||||| | ||||| || || |||||||||||||||||||||  |  | | |      |       |||  ||   ||       | ||| ||    |  |     | |||   |  |  || ||||  |    | || 
CATTTATGGGGTACACGATGAGGCCAAGGACAAGGCATTTGAGTTGGAAATGAGCTGGGTTTGTGAGGAGTCAAACCGCCAGCATCAGAAGgtaatctcttgaatttatcaagatcaagaaacattaacttaactcatatcttgaagacatctaccctgttgattgcacccatgctcactagctggatagc

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|211317863|gb|FK969337.1|FK969337

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|211317862|gb|FK969336.1|FK969336

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|211317857|gb|FK969331.1|FK969331

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|16919551|gb|BM074245.1|BM074245

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|211317861|gb|FK969335.1|FK969335

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|211404206|gb|FL443972.1|FL443972

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|211317859|gb|FK969333.1|FK969333

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|211079760|gb|FK950720.1|FK950720

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|32933640|gb|CF038452.1|CF038452

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|211169213|gb|FL479845.1|FL479845

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|211317856|gb|FK969330.1|FK969330

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|211317864|gb|FK969338.1|FK969338

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|211317854|gb|FK969328.1|FK969328

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|166676765|gb|EG166808.1|EG166808

EST:     TCGAACCGCCAGCAATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCT
genomic: TCGAACCGCCAGC-ATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCT

EST: gi|211317865|gb|FK969339.1|FK969339

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|12969059|gb|BG266004.1|BG266004

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAAT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAAT

EST: gi|211317860|gb|FK969334.1|FK969334

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

EST: gi|211317855|gb|FK969329.1|FK969329

EST:     AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAG                         GTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT
genomic: AGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTT

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 323

AATTTATGGAGTGCATGACGAATCCAAGGACAAAGCTTTTGAGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtggg ... tgtcatacagGTTCCGAATGAATTGTTGGAGCAGGCCAAAGCTGCTGCTCAGGCAGCTCTTGAGGAGATGGATGCTGACTAAGAAACATGACAAATATGCCCATGCTTCA

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 278

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 341

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 302

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTTATGGAGTGCATGACGAATCCAAGGACAAAGCTTTTGAGTTGGAGTTGAGCTGGATCTGTGATGAATCGAACCGCCAGCATCAGAAGgtaccgtgggaccagatattcaggcgaagaatggcctctctatgtttctcgatttgaatttaaagctgaaacttctttggtcacctgtcatacag

- - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA